Incidental Mutation 'R6333:Pcdh1'
| ID |
513261 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdh1
|
| Ensembl Gene |
ENSMUSG00000051375 |
| Gene Name |
protocadherin 1 |
| Synonyms |
2010005A06Rik |
| MMRRC Submission |
044487-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.365)
|
| Stock # |
R6333 (G1)
|
| Quality Score |
188.009 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
38318967-38345023 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 38331860 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 381
(V381A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000125576
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000057185]
[ENSMUST00000159405]
[ENSMUST00000160721]
[ENSMUST00000161701]
[ENSMUST00000193828]
[ENSMUST00000194312]
|
| AlphaFold |
Q8CFX3 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000057185
AA Change: V520A
PolyPhen 2
Score 0.027 (Sensitivity: 0.95; Specificity: 0.81)
|
| SMART Domains |
Protein: ENSMUSP00000055199
Gene: ENSMUSG00000051375
AA Change: V520A
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
33 |
N/A |
INTRINSIC |
|
Pfam:Cadherin_2
|
36 |
120 |
2e-8 |
PFAM |
|
CA
|
168 |
256 |
5.18e-18 |
SMART |
|
CA
|
280 |
363 |
5.68e-24 |
SMART |
|
CA
|
395 |
482 |
1.84e-23 |
SMART |
|
CA
|
506 |
588 |
2.99e-32 |
SMART |
|
CA
|
612 |
691 |
9.36e-25 |
SMART |
|
CA
|
717 |
798 |
9.9e-15 |
SMART |
|
transmembrane domain
|
830 |
852 |
N/A |
INTRINSIC |
|
low complexity region
|
876 |
903 |
N/A |
INTRINSIC |
|
low complexity region
|
951 |
964 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000159405
AA Change: V520A
PolyPhen 2
Score 0.027 (Sensitivity: 0.95; Specificity: 0.81)
|
| SMART Domains |
Protein: ENSMUSP00000125309
Gene: ENSMUSG00000051375
AA Change: V520A
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
33 |
N/A |
INTRINSIC |
|
Pfam:Cadherin_2
|
36 |
120 |
2e-8 |
PFAM |
|
CA
|
168 |
256 |
5.18e-18 |
SMART |
|
CA
|
280 |
363 |
5.68e-24 |
SMART |
|
CA
|
395 |
482 |
1.84e-23 |
SMART |
|
CA
|
506 |
588 |
2.99e-32 |
SMART |
|
CA
|
612 |
691 |
9.36e-25 |
SMART |
|
CA
|
717 |
798 |
9.9e-15 |
SMART |
|
transmembrane domain
|
830 |
852 |
N/A |
INTRINSIC |
|
low complexity region
|
876 |
903 |
N/A |
INTRINSIC |
|
low complexity region
|
951 |
964 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000160721
|
| SMART Domains |
Protein: ENSMUSP00000124732
Gene: ENSMUSG00000051375
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
33 |
N/A |
INTRINSIC |
|
Pfam:Cadherin_2
|
36 |
120 |
9.9e-10 |
PFAM |
|
CA
|
168 |
256 |
5.18e-18 |
SMART |
|
low complexity region
|
310 |
321 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000161701
AA Change: V381A
PolyPhen 2
Score 0.247 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000125576
Gene: ENSMUSG00000051375
AA Change: V381A
| Domain | Start | End | E-Value | Type |
|---|
|
CA
|
29 |
117 |
5.18e-18 |
SMART |
|
CA
|
141 |
224 |
5.68e-24 |
SMART |
|
CA
|
256 |
343 |
1.84e-23 |
SMART |
|
CA
|
367 |
449 |
2.99e-32 |
SMART |
|
CA
|
473 |
552 |
9.36e-25 |
SMART |
|
CA
|
578 |
659 |
9.9e-15 |
SMART |
|
transmembrane domain
|
691 |
713 |
N/A |
INTRINSIC |
|
low complexity region
|
737 |
764 |
N/A |
INTRINSIC |
|
low complexity region
|
812 |
825 |
N/A |
INTRINSIC |
|
low complexity region
|
903 |
914 |
N/A |
INTRINSIC |
|
low complexity region
|
1029 |
1040 |
N/A |
INTRINSIC |
|
low complexity region
|
1059 |
1071 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000193828
|
| SMART Domains |
Protein: ENSMUSP00000142328
Gene: ENSMUSG00000051375
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
18 |
48 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000194312
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.7%
- 10x: 97.9%
- 20x: 93.2%
|
| Validation Efficiency |
98% (50/51) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the protocadherin subfamily within the cadherin superfamily. The encoded protein is a membrane protein found at cell-cell boundaries. It is involved in neural cell adhesion, suggesting a possible role in neuronal development. The protein includes an extracelllular region, containing 7 cadherin-like domains, a transmembrane region and a C-terminal cytoplasmic region. Cells expressing the protein showed cell aggregation activity. Alternative splicing occurs in this gene. [provided by RefSeq, Jul 2008]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4931406C07Rik |
T |
C |
9: 15,203,372 (GRCm39) |
K111R |
probably benign |
Het |
| Abhd18 |
A |
G |
3: 40,888,218 (GRCm39) |
Y354C |
probably benign |
Het |
| Acap1 |
T |
C |
11: 69,774,427 (GRCm39) |
I424V |
possibly damaging |
Het |
| AI182371 |
A |
T |
2: 34,975,281 (GRCm39) |
I306K |
probably damaging |
Het |
| Asb4 |
G |
A |
6: 5,423,597 (GRCm39) |
R248H |
probably damaging |
Het |
| Brd7 |
T |
C |
8: 89,071,819 (GRCm39) |
T349A |
probably damaging |
Het |
| Bub1b |
T |
C |
2: 118,428,944 (GRCm39) |
|
probably null |
Het |
| Cep85l |
G |
A |
10: 53,225,197 (GRCm39) |
Q131* |
probably null |
Het |
| Chmp2b |
T |
A |
16: 65,337,136 (GRCm39) |
M178L |
possibly damaging |
Het |
| Chrnb3 |
A |
G |
8: 27,883,355 (GRCm39) |
N84D |
probably damaging |
Het |
| Clec4b2 |
A |
T |
6: 123,177,637 (GRCm39) |
|
probably null |
Het |
| Defa34 |
T |
C |
8: 22,155,862 (GRCm39) |
V17A |
probably benign |
Het |
| Dnah3 |
A |
T |
7: 119,653,856 (GRCm39) |
L947Q |
probably damaging |
Het |
| Dynlt2a1 |
G |
A |
17: 15,261,717 (GRCm39) |
|
probably benign |
Het |
| Ell |
A |
G |
8: 71,044,188 (GRCm39) |
Y578C |
probably damaging |
Het |
| Esp36 |
T |
A |
17: 38,728,135 (GRCm39) |
M49L |
probably benign |
Het |
| Fbxw19 |
A |
T |
9: 109,323,751 (GRCm39) |
W75R |
probably benign |
Het |
| Fcgr4 |
A |
G |
1: 170,856,838 (GRCm39) |
Y235C |
probably damaging |
Het |
| Gm10110 |
A |
C |
14: 90,135,733 (GRCm39) |
|
noncoding transcript |
Het |
| Gm13030 |
A |
T |
4: 138,598,708 (GRCm39) |
|
probably null |
Het |
| Hdac9 |
T |
C |
12: 34,102,323 (GRCm39) |
M1058V |
probably damaging |
Het |
| Hsd3b6 |
A |
G |
3: 98,713,540 (GRCm39) |
F253S |
probably damaging |
Het |
| Hspg2 |
T |
C |
4: 137,289,266 (GRCm39) |
Y3794H |
probably damaging |
Het |
| Mark4 |
G |
A |
7: 19,177,208 (GRCm39) |
T207M |
probably damaging |
Het |
| Mme |
A |
G |
3: 63,249,382 (GRCm39) |
T304A |
probably benign |
Het |
| Neb |
A |
G |
2: 52,148,275 (GRCm39) |
L2657P |
probably damaging |
Het |
| Nufip1 |
A |
C |
14: 76,349,425 (GRCm39) |
K152N |
probably damaging |
Het |
| Pdss1 |
A |
G |
2: 22,791,778 (GRCm39) |
T30A |
probably damaging |
Het |
| Plrg1 |
A |
G |
3: 82,964,102 (GRCm39) |
T12A |
probably damaging |
Het |
| Ppig |
C |
T |
2: 69,579,902 (GRCm39) |
H479Y |
unknown |
Het |
| Prokr2 |
A |
G |
2: 132,215,898 (GRCm39) |
F188L |
probably damaging |
Het |
| Prss39 |
A |
G |
1: 34,539,150 (GRCm39) |
N130S |
probably benign |
Het |
| Ptar1 |
G |
A |
19: 23,671,686 (GRCm39) |
D30N |
possibly damaging |
Het |
| Rai14 |
G |
T |
15: 10,575,022 (GRCm39) |
Y645* |
probably null |
Het |
| Rnasek |
T |
C |
11: 70,129,252 (GRCm39) |
Y67C |
probably damaging |
Het |
| Rnd2 |
C |
T |
11: 101,359,825 (GRCm39) |
L57F |
probably damaging |
Het |
| Rnf213 |
T |
C |
11: 119,354,192 (GRCm39) |
V4023A |
probably damaging |
Het |
| Sash3 |
C |
T |
X: 47,248,398 (GRCm39) |
L307F |
probably damaging |
Homo |
| Sctr |
T |
C |
1: 119,984,182 (GRCm39) |
F357L |
probably damaging |
Het |
| Sec14l5 |
G |
A |
16: 4,984,908 (GRCm39) |
V85I |
probably benign |
Het |
| Shld2 |
G |
A |
14: 33,989,565 (GRCm39) |
T447M |
probably damaging |
Het |
| Sirpd |
T |
C |
3: 15,385,671 (GRCm39) |
Y77C |
probably damaging |
Het |
| Spag8 |
T |
C |
4: 43,653,186 (GRCm39) |
|
probably benign |
Het |
| Tbc1d2 |
T |
C |
4: 46,620,736 (GRCm39) |
D358G |
possibly damaging |
Het |
| Tenm4 |
A |
G |
7: 96,423,331 (GRCm39) |
T672A |
probably damaging |
Het |
| Tent2 |
G |
A |
13: 93,322,821 (GRCm39) |
Q43* |
probably null |
Het |
| Trmt1l |
T |
A |
1: 151,329,685 (GRCm39) |
S543T |
probably benign |
Het |
| Ube4b |
A |
G |
4: 149,432,494 (GRCm39) |
F810S |
probably damaging |
Het |
| Vmn2r104 |
C |
T |
17: 20,249,848 (GRCm39) |
V808I |
probably benign |
Het |
| Zfp3 |
T |
A |
11: 70,662,266 (GRCm39) |
I75N |
probably benign |
Het |
| Zwint |
A |
G |
10: 72,490,784 (GRCm39) |
|
probably benign |
Het |
|
| Other mutations in Pcdh1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00714:Pcdh1
|
APN |
18 |
38,331,782 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
IGL00919:Pcdh1
|
APN |
18 |
38,335,865 (GRCm39) |
nonsense |
probably null |
|
|
IGL01744:Pcdh1
|
APN |
18 |
38,336,302 (GRCm39) |
missense |
probably damaging |
1.00 |
|
PIT4260001:Pcdh1
|
UTSW |
18 |
38,336,419 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R0542:Pcdh1
|
UTSW |
18 |
38,322,975 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1449:Pcdh1
|
UTSW |
18 |
38,322,929 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1540:Pcdh1
|
UTSW |
18 |
38,322,779 (GRCm39) |
missense |
probably benign |
0.01 |
|
R1642:Pcdh1
|
UTSW |
18 |
38,332,283 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
R1672:Pcdh1
|
UTSW |
18 |
38,325,233 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1695:Pcdh1
|
UTSW |
18 |
38,335,921 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1727:Pcdh1
|
UTSW |
18 |
38,336,085 (GRCm39) |
nonsense |
probably null |
|
|
R1781:Pcdh1
|
UTSW |
18 |
38,322,977 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1793:Pcdh1
|
UTSW |
18 |
38,331,938 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1839:Pcdh1
|
UTSW |
18 |
38,332,538 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
R1843:Pcdh1
|
UTSW |
18 |
38,325,278 (GRCm39) |
splice site |
probably null |
|
|
R1882:Pcdh1
|
UTSW |
18 |
38,335,895 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
R2261:Pcdh1
|
UTSW |
18 |
38,331,710 (GRCm39) |
missense |
probably benign |
0.01 |
|
R2262:Pcdh1
|
UTSW |
18 |
38,331,710 (GRCm39) |
missense |
probably benign |
0.01 |
|
R2263:Pcdh1
|
UTSW |
18 |
38,331,710 (GRCm39) |
missense |
probably benign |
0.01 |
|
R2511:Pcdh1
|
UTSW |
18 |
38,332,532 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R2937:Pcdh1
|
UTSW |
18 |
38,322,815 (GRCm39) |
missense |
probably benign |
0.40 |
|
R3941:Pcdh1
|
UTSW |
18 |
38,332,511 (GRCm39) |
missense |
probably benign |
0.02 |
|
R3942:Pcdh1
|
UTSW |
18 |
38,332,511 (GRCm39) |
missense |
probably benign |
0.02 |
|
R4057:Pcdh1
|
UTSW |
18 |
38,331,950 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4155:Pcdh1
|
UTSW |
18 |
38,336,159 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R4169:Pcdh1
|
UTSW |
18 |
38,331,358 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4617:Pcdh1
|
UTSW |
18 |
38,330,913 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4690:Pcdh1
|
UTSW |
18 |
38,336,528 (GRCm39) |
missense |
probably benign |
0.33 |
|
R4825:Pcdh1
|
UTSW |
18 |
38,322,912 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R5201:Pcdh1
|
UTSW |
18 |
38,331,971 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R5266:Pcdh1
|
UTSW |
18 |
38,325,252 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5267:Pcdh1
|
UTSW |
18 |
38,325,252 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5351:Pcdh1
|
UTSW |
18 |
38,330,819 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5568:Pcdh1
|
UTSW |
18 |
38,330,420 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5729:Pcdh1
|
UTSW |
18 |
38,335,999 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5731:Pcdh1
|
UTSW |
18 |
38,331,651 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6043:Pcdh1
|
UTSW |
18 |
38,336,327 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R6278:Pcdh1
|
UTSW |
18 |
38,332,263 (GRCm39) |
missense |
probably benign |
0.29 |
|
R6498:Pcdh1
|
UTSW |
18 |
38,330,490 (GRCm39) |
missense |
probably benign |
0.18 |
|
R6937:Pcdh1
|
UTSW |
18 |
38,336,528 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R6994:Pcdh1
|
UTSW |
18 |
38,331,553 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7242:Pcdh1
|
UTSW |
18 |
38,336,270 (GRCm39) |
missense |
probably benign |
0.06 |
|
R7289:Pcdh1
|
UTSW |
18 |
38,322,966 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7391:Pcdh1
|
UTSW |
18 |
38,335,838 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R7702:Pcdh1
|
UTSW |
18 |
38,336,569 (GRCm39) |
missense |
unknown |
|
|
R7738:Pcdh1
|
UTSW |
18 |
38,330,529 (GRCm39) |
missense |
probably benign |
0.02 |
|
R7849:Pcdh1
|
UTSW |
18 |
38,322,662 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7941:Pcdh1
|
UTSW |
18 |
38,332,133 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8109:Pcdh1
|
UTSW |
18 |
38,332,049 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8675:Pcdh1
|
UTSW |
18 |
38,332,229 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8851:Pcdh1
|
UTSW |
18 |
38,325,155 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8947:Pcdh1
|
UTSW |
18 |
38,332,073 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R9443:Pcdh1
|
UTSW |
18 |
38,330,633 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9448:Pcdh1
|
UTSW |
18 |
38,330,492 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9608:Pcdh1
|
UTSW |
18 |
38,330,904 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
X0027:Pcdh1
|
UTSW |
18 |
38,322,841 (GRCm39) |
nonsense |
probably null |
|
|
Z1088:Pcdh1
|
UTSW |
18 |
38,331,120 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1176:Pcdh1
|
UTSW |
18 |
38,331,741 (GRCm39) |
missense |
possibly damaging |
0.79 |
|
| Predicted Primers |
PCR Primer
(F):5'- GAGCACATTGACGAGGACTG -3'
(R):5'- AGACTATACCATCGAGATCGTGG -3'
Sequencing Primer
(F):5'- ACATTGACGAGGACTGTGGCTG -3'
(R):5'- CTATACCATCGAGATCGTGGCTGTG -3'
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| Posted On |
2018-04-27 |
Incidental Mutation